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Why Rattlesnakes?

Why Rattlesnakes?. Model organisms for adaptation to low-energy lifestyles Low metabolism- down-regulate whole organ systems Starvation bouts up to two years Pit Vipers: rapid rates of evolution of mitochondrial genome. Applications:.

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Why Rattlesnakes?

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  1. Why Rattlesnakes? • Model organisms foradaptation to low-energy lifestyles • Low metabolism-down-regulate whole organ systems • Starvation bouts up to two years • Pit Vipers: rapid rates of evolution of mitochondrial genome

  2. Applications: • Transcriptomics of specific tissues using RNASeq during starvation • Reprogram the transcriptome of muscles during prolonged starvation • Reactivation of digestive system upon feeding • Comparative biology in medical research. • Chicken was one of the first vertebrate, non-mammal genomes sequenced • Assemblies of green anole lizard and python.

  3. Progress • Began with pilot 454 sequencing for repeats • Collaboration with faculty at KAUST • Illumina Sequencing • Call by MCBIOS for community project • Share in the assembly and annotation, for training of students and development of programs, publications, funding

  4. Current Data

  5. Transcriptome Assembly • Transcriptome • 50mer assembly 11,000 contigs • No BLAST data yet • Ptitsyn • 10237 with significant BLAST scores • 888 with no annotation

  6. Trinity Assembly

  7. Assembly data • Genome • Velvet on Blacklight (Jeff Pummill) • 43 Kmer; does not include 454 data

  8. Assembly data (cont’d)

  9. Where are the data • Submitted to GenbankBioproject/SRA • Available on secure FTP site at uark.edu • See drhoads@uark.edu for ID and password

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